Retrieve the lowest common taxon and rank for a given taxon name or ID
Retrieve the lowest common taxon and rank for a given taxon name or ID
lowest_common(...) ## Default S3 method: lowest_common( sci_id, db = NULL, rows = NA, class_list = NULL, low_rank = NULL, x = NULL, ... ) ## S3 method for class 'uid' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...) ## S3 method for class 'tsn' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...) ## S3 method for class 'gbifid' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...) ## S3 method for class 'tolid' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...)
... |
Other arguments passed to |
sci_id |
Vector of taxa names (character) or id (character or numeric) to query. |
db |
character; database to query. either |
rows |
(numeric) Any number from 1 to infinity. If the default NA, all rows are considered. Note that this parameter is ignored if you pass in a taxonomic id of any of the acceptable classes: tsn, gbifid, tolid. NCBI has a method for this function but rows doesn't work. |
class_list |
(list) A list of classifications, as returned from
|
low_rank |
(character) taxonomic rank to return, of length 1 |
x |
Deprecated, see |
NA when no match, or a data.frame with columns
name
rank
id
See taxize-authentication for help on authentication
Jimmy O'Donnell jodonnellbio@gmail.com Scott Chamberlain
## Not run:
id <- c("9031", "9823", "9606", "9470")
id_class <- classification(id, db = 'ncbi')
lowest_common(id[2:4], db = "ncbi")
lowest_common(id[2:4], db = "ncbi", low_rank = 'class')
lowest_common(id[2:4], db = "ncbi", low_rank = 'family')
lowest_common(id[2:4], class_list = id_class)
lowest_common(id[2:4], class_list = id_class, low_rank = 'class')
lowest_common(id[2:4], class_list = id_class, low_rank = 'family')
# TOL
taxa <- c("Angraecum sesquipedale", "Dracula vampira",
"Masdevallia coccinea")
(cls <- classification(taxa, db = "tol"))
lowest_common(taxa, db = "tol", class_list = cls)
lowest_common(get_tolid(taxa), class_list = cls)
xx <- get_tolid(taxa)
lowest_common(xx, class_list = cls)
spp <- c("Sus scrofa", "Homo sapiens", "Nycticebus coucang")
lowest_common(spp, db = "ncbi")
lowest_common(get_uid(spp))
lowest_common(spp, db = "itis")
lowest_common(get_tsn(spp))
gbifid <- c("2704179", "3119195")
lowest_common(gbifid, db = "gbif")
spp <- c("Poa annua", "Helianthus annuus")
lowest_common(spp, db = "gbif")
lowest_common(get_gbifid(spp))
cool_orchid <- c("Angraecum sesquipedale", "Dracula vampira",
"Masdevallia coccinea")
orchid_ncbi <- get_uid(cool_orchid)
orchid_gbif <- get_gbifid(cool_orchid)
cool_orchids2 <- c("Domingoa haematochila", "Gymnadenia conopsea",
"Masdevallia coccinea")
orchid_itis <- get_tsn(cool_orchids2)
orchid_hier_ncbi <- classification(orchid_ncbi, db = 'ncbi')
orchid_hier_gbif <- classification(orchid_gbif, db = 'gbif')
orchid_hier_itis <- classification(orchid_itis, db = 'itis')
lowest_common(orchid_ncbi, low_rank = 'class')
lowest_common(orchid_ncbi, class_list = orchid_hier_ncbi,
low_rank = 'class')
lowest_common(orchid_gbif, low_rank = 'class')
lowest_common(orchid_gbif, orchid_hier_gbif, low_rank = 'class')
lowest_common(get_uid(cool_orchid), low_rank = 'class')
lowest_common(get_uid(cool_orchid), low_rank = 'family')
lowest_common(orchid_ncbi, class_list = orchid_hier_ncbi,
low_rank = 'subfamily')
lowest_common(orchid_gbif, class_list = orchid_hier_gbif,
low_rank = 'subfamily')
lowest_common(orchid_itis, class_list = orchid_hier_itis,
low_rank = 'class')
## Pass in sci. names
nms <- c("Angraecum sesquipedale", "Dracula vampira", "Masdevallia coccinea")
lowest_common(x = nms, db = "ncbi")
lowest_common(x = nms, db = "gbif")
# lowest_common(x = nms, db = "itis")
## NAs due to taxon not found, stops with error message
# lowest_common(orchid_itis, db = "itis")
# lowest_common(get_tsn(cool_orchid))
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.